Here is a site I pulled up on box turtes with shell rot and other illnesses-->http://boxturtlesite.org/heal.html
And here is the section on shell rot-->
Shell rot..
Check the turtle often for signs of shell rot. Shell rot is caused by fungus or bacteria. The bacteria that cause shell rot often enter small cuts or cracks in the plastron. Once under the keratin layer of the shell, bacteria begins to grow on the bone. Soon the keratin layer separates from the bone and a smelly, slick area of shell rot is exposed. The best way to prevent this is to clean and disinfect any cuts on the turtle’s shell. I regularly wash my turtles with chlorahexine cleanser. I apply triple antibiotic cream onto any cuts to shell and skin that appears to be infected. Also, the turtle's living area should be kept as clean as possible. All feces and uneaten food should be removed as soon as possible. The water should be changed daily. Don’t give bacteria a place to live and thrive.
Shell rot can be hard to detect in box turtles unless you inspect for it. If shell rot is found, a vigorous regimen of cleaning and medication is necessary. Remove any peeling keratin from the area. The thin keratin layer usually pops right off. What is exposed is bone with bacteria growing on it. Gently clean the area with dilute betadine or a chlorahexine cleanser and apply triple antibiotic cream to the area. Protect the area so it stays clean. Do this for several weeks until the bone has had a chance to calcify. The bone is a living, porous material and will heal and protect itself if given the opportunity. If the area of shell rot is large, the turtle should be taken to a reptile veterinarian for possible injectable antibiotics. Other diseases of the bone or blood can develop from shell rot.
Sorry if it's a little long but I tried to help..Here is a pic: Shell rot
Check the turtle often for signs of shell rot. Shell rot is caused by fungus or bacteria. The bacteria that cause shell rot often enter small cuts or cracks in the plastron. Once under the keratin layer of the shell, bacteria begins to grow on the bone. Soon the keratin layer separates from the bone and a smelly, slick area of shell rot is exposed. The best way to prevent this is to clean and disinfect any cuts on the turtle’s shell. I regularly wash my turtles with chlorahexine cleanser. I apply triple antibiotic cream onto any cuts to shell and skin that appears to be infected. Also, the turtle's living area should be kept as clean as possible. All feces and uneaten food should be removed as soon as possible. The water should be changed daily. Don’t give bacteria a place to live and thrive.
Shell rot can be hard to detect in box turtles unless you inspect for it. If shell rot is found, a vigorous regimen of cleaning and medication is necessary. Remove any peeling keratin from the area. The thin keratin layer usually pops right off. What is exposed is bone with bacteria growing on it. Gently clean the area with dilute betadine or a chlorahexine cleanser and apply triple antibiotic cream to the area. Protect the area so it stays clean. Do this for several weeks until the bone has had a chance to calcify. The bone is a living, porous material and will heal and protect itself if given the opportunity. If the area of shell rot is large, the turtle should be taken to a reptile veterinarian for possible injectable antibiotics. Other diseases of the bone or blood can develop from shell rot.
I hope I've helped and I'm sorry to hear about your turtle. Hope things pull through as well..
There is also a picture on that site w/a box turtle with shell rot.